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   &#160;<span id="projectnumber">2.x</span>
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&#160;

<h3><a id="index_a"></a>- a -</h3><ul>
<li>ArgumentHandler()
: <a class="el" href="class_argument_handler.html#a2657983b12529181db92512d3a6fc1fa">ArgumentHandler</a>
</li>
<li>argumentTest()
: <a class="el" href="class_argument_handler.html#aed3ea207ece08d71c49613911ac8b711">ArgumentHandler</a>
</li>
<li>ArrayHeapExtMem()
: <a class="el" href="class_array_heap_ext_mem.html#a3a5ef6bdef74f27b29dba5c29996baf0">ArrayHeapExtMem</a>
</li>
</ul>


<h3><a id="index_b"></a>- b -</h3><ul>
<li>BinaryHeap()
: <a class="el" href="class_binary_heap.html#a7869a94b091c236c876f2446d7e51b66">BinaryHeap</a>
</li>
<li>BinaryHeap_FourInts()
: <a class="el" href="class_binary_heap___four_ints.html#accd7827f6c708ef7dbfdc8c0eb1e547b">BinaryHeap_FourInts</a>
</li>
<li>BinaryHeap_IntKey_TwoInts()
: <a class="el" href="class_binary_heap___int_key___two_ints.html#aa98d9cfefd8317c6ecb5a1f6d271e27b">BinaryHeap_IntKey_TwoInts</a>
</li>
<li>BinaryHeap_TwoInts()
: <a class="el" href="class_binary_heap___two_ints.html#ae1e39bfeaa140bd4608796e1c80491f1">BinaryHeap_TwoInts</a>
</li>
<li>binHeapFourTest()
: <a class="el" href="class_binary_heap___four_ints.html#ae75fa6b6aa704e4091ab93daf783f5b2">BinaryHeap_FourInts</a>
</li>
<li>binHeapTest()
: <a class="el" href="class_binary_heap.html#a176296b32feaa157c1d6896ba89f7227">BinaryHeap</a>
</li>
<li>binHeapTwoTest()
: <a class="el" href="class_binary_heap___int_key___two_ints.html#ab89ee10199056b3f2dd321869ceb7575">BinaryHeap_IntKey_TwoInts</a>
, <a class="el" href="class_binary_heap___two_ints.html#a7105a0874acdf81833a22cb55230db9d">BinaryHeap_TwoInts</a>
</li>
<li>build()
: <a class="el" href="class_tree_builder_bin_heap.html#a55103dd4bc84a5338920f08e7d943001">TreeBuilderBinHeap</a>
, <a class="el" href="class_tree_builder_ext_mem.html#a1209ad5479e3822de6311cbd39cb897f">TreeBuilderExtMem</a>
</li>
<li>buildAgain()
: <a class="el" href="class_binary_heap___four_ints.html#a2a92d6d547ccffa9e10138d0d7ac50e5">BinaryHeap_FourInts</a>
, <a class="el" href="class_binary_heap___two_ints.html#a8f4ba6e7b7568543be697b132c04b945">BinaryHeap_TwoInts</a>
</li>
<li>buildNodeList()
: <a class="el" href="class_candidate_heap.html#a3be4ad358ceebf062311c31cdfc7b327">CandidateHeap</a>
</li>
<li>buildTreeString()
: <a class="el" href="class_tree_node.html#a00d167b78ddd279f0b580de621b4dc93">TreeNode</a>
</li>
</ul>


<h3><a id="index_c"></a>- c -</h3><ul>
<li>calc()
: <a class="el" href="class_distance_calculator.html#a3103ea39f1b1dbdbb7e23afd2adbd959">DistanceCalculator</a>
</li>
<li>calcDeltaValues()
: <a class="el" href="class_candidate_heap.html#a5e855706e9f4ae3344c3d4d40ca25efd">CandidateHeap</a>
</li>
<li>CandidateHeap()
: <a class="el" href="class_candidate_heap.html#a7ddaa04ab82c9821d4ac63bbc2445f9c">CandidateHeap</a>
</li>
<li>chopBottomK()
: <a class="el" href="class_binary_heap___two_ints.html#a03c9fb4cbdfd9942b59ee9285ae51c93">BinaryHeap_TwoInts</a>
</li>
<li>clear()
: <a class="el" href="class_candidate_heap.html#ac60355b267aeadb043cf2d1343f0d0a4">CandidateHeap</a>
, <a class="el" href="class_stack.html#adab1284b8929385d4020356fb52c8139">Stack</a>
</li>
<li>clearAndInitialize()
: <a class="el" href="class_array_heap_ext_mem.html#a4f8d3d0869f1fa215d25e2cbcee0266d">ArrayHeapExtMem</a>
</li>
<li>closeAndDeleteFile()
: <a class="el" href="class_array_heap_ext_mem.html#a8a6d92421203923ef902b3bb78262a84">ArrayHeapExtMem</a>
</li>
<li>compareTo()
: <a class="el" href="class_slot_pair.html#a1304d88a845660a897d8ad3abc9acb17">SlotPair</a>
</li>
</ul>


<h3><a id="index_d"></a>- d -</h3><ul>
<li>deleteAll()
: <a class="el" href="class_array_heap_ext_mem.html#a49b44e6cebc42ae0ead6ae51fcde6a87">ArrayHeapExtMem</a>
</li>
<li>deleteMin()
: <a class="el" href="class_binary_heap.html#a37e19e8dadb4e66fb148fed5b56aa86e">BinaryHeap</a>
, <a class="el" href="class_binary_heap___four_ints.html#a228e5e686175ef82acc7ed61a15c6b75">BinaryHeap_FourInts</a>
, <a class="el" href="class_binary_heap___int_key___two_ints.html#a2c6c4999917c20d9daee36e60aae4908">BinaryHeap_IntKey_TwoInts</a>
, <a class="el" href="class_binary_heap___two_ints.html#a4d9f2c086da3211a124893f2231fe427">BinaryHeap_TwoInts</a>
</li>
<li>describeHeap()
: <a class="el" href="class_array_heap_ext_mem.html#abeadfba6f8a622814d9750c72f31fe3b">ArrayHeapExtMem</a>
</li>
<li>DistanceCalculator()
: <a class="el" href="class_distance_calculator.html#a2a8861e559827f4a9324b854edc13e58">DistanceCalculator</a>
</li>
<li>DistanceReader()
: <a class="el" href="class_distance_reader.html#a72990b5a7a716c51bc9800babb1ad6ed">DistanceReader</a>
</li>
<li>DistanceReaderExtMem()
: <a class="el" href="class_distance_reader_ext_mem.html#aefe2b4edd62f967e62a40ce70587876d">DistanceReaderExtMem</a>
</li>
<li>doJob()
: <a class="el" href="class_tree_builder_manager.html#a82bd45375c241cc86bf5d26f4fef05ed">TreeBuilderManager</a>
</li>
</ul>


<h3><a id="index_f"></a>- f -</h3><ul>
<li>finishMerging()
: <a class="el" href="class_tree_builder.html#a1febaf1b495ebfb94b0017111560f45c">TreeBuilder</a>
</li>
</ul>


<h3><a id="index_g"></a>- g -</h3><ul>
<li>getAbort()
: <a class="el" href="class_argument_handler.html#ad6143cf6a96ca5cc6aeb97f432bc629d">ArgumentHandler</a>
</li>
<li>getAlphabetType()
: <a class="el" href="class_argument_handler.html#a8b8d3d08a48c31c010aa80095f85e7cf">ArgumentHandler</a>
</li>
<li>getAlphType()
: <a class="el" href="class_sequence_file_reader.html#a19cd3893e28924779bfcb74a1cece03b">SequenceFileReader</a>
</li>
<li>getBinaryHeapWithMin()
: <a class="el" href="class_array_heap_ext_mem.html#ae2586a4b61b0cda1447748fb0e0083d0">ArrayHeapExtMem</a>
</li>
<li>getCorrectionType()
: <a class="el" href="class_argument_handler.html#ad2b8028126c07aabb8603c44594ffaa6">ArgumentHandler</a>
</li>
<li>getInputFile()
: <a class="el" href="class_argument_handler.html#ad651123ca891c60ec98111817e38b06a">ArgumentHandler</a>
</li>
<li>getInputType()
: <a class="el" href="class_argument_handler.html#a32c069acf9792739ceb10c87edf22ddc">ArgumentHandler</a>
</li>
<li>getInverseAlphabet()
: <a class="el" href="class_distance_calculator.html#a852203aaa2f7eb7faf53cc52245244f1">DistanceCalculator</a>
</li>
<li>getMethod()
: <a class="el" href="class_argument_handler.html#ac6b6ce1eb3d6fee43314823c8c3e9e6c">ArgumentHandler</a>
</li>
<li>getNames()
: <a class="el" href="class_sequence_file_reader.html#a90a7fe721e3311573775ab8f7c946ec9">SequenceFileReader</a>
</li>
<li>getNJTmpDir()
: <a class="el" href="class_argument_handler.html#a242123ae240bca20b782c544416e2fc3">ArgumentHandler</a>
</li>
<li>getNumThreads()
: <a class="el" href="class_argument_handler.html#a56ce7d11969a9efb741fa10fc14deed2">ArgumentHandler</a>
</li>
<li>getOutputFile()
: <a class="el" href="class_argument_handler.html#a1c8fbd4a0c2b3d4235c3ef8b83fd43b8">ArgumentHandler</a>
</li>
<li>getOutputType()
: <a class="el" href="class_argument_handler.html#ab0837386ce1c1f76280c9917572989dc">ArgumentHandler</a>
</li>
<li>getSeqs()
: <a class="el" href="class_sequence_file_reader.html#ac6ddf2c86a6e8c25f21d9e1381cb08ce">SequenceFileReader</a>
</li>
<li>getUseSSE()
: <a class="el" href="class_argument_handler.html#a817493c9c676890ac210e1384191828c">ArgumentHandler</a>
</li>
</ul>


<h3><a id="index_i"></a>- i -</h3><ul>
<li>insert()
: <a class="el" href="class_array_heap_ext_mem.html#a70370771be3fc71f96fe0c2adfbbfdee">ArrayHeapExtMem</a>
, <a class="el" href="class_binary_heap.html#a146554bd398e659498861fcfbcafd645">BinaryHeap</a>
, <a class="el" href="class_binary_heap___four_ints.html#a06e1de8a41a21e445e4eddca11bd0838">BinaryHeap_FourInts</a>
, <a class="el" href="class_binary_heap___int_key___two_ints.html#a6226095081ed11a6a838e078079e19b7">BinaryHeap_IntKey_TwoInts</a>
, <a class="el" href="class_binary_heap___two_ints.html#aeb013e054d6cf4e8b21baf1ae10b12b4">BinaryHeap_TwoInts</a>
, <a class="el" href="class_candidate_heap.html#a41a89d7d4a17b8dbdb26f8d82664000c">CandidateHeap</a>
</li>
<li>isEmpty()
: <a class="el" href="class_array_heap_ext_mem.html#a335bcdde7c416d7bfea8175cafefb120">ArrayHeapExtMem</a>
, <a class="el" href="class_binary_heap.html#a41ac81a66982236c6b0428b3f0bf14cf">BinaryHeap</a>
, <a class="el" href="class_binary_heap___four_ints.html#a82e668d4fc3d8a75499c347eb061038d">BinaryHeap_FourInts</a>
, <a class="el" href="class_binary_heap___int_key___two_ints.html#aa0de4bdcaa070ea51c231f469caff839">BinaryHeap_IntKey_TwoInts</a>
, <a class="el" href="class_binary_heap___two_ints.html#a66fa2c6397631c8e2571efb9b9635ff9">BinaryHeap_TwoInts</a>
, <a class="el" href="class_stack.html#acfd33dabc532e2706dea1699a4de2636">Stack</a>
</li>
</ul>


<h3><a id="index_l"></a>- l -</h3><ul>
<li>length()
: <a class="el" href="class_stack.html#a3eb1a8501ea96c64f5244bba86d9c652">Stack</a>
</li>
</ul>


<h3><a id="index_m"></a>- m -</h3><ul>
<li>makeEmpty()
: <a class="el" href="class_binary_heap.html#ae1d3eb2f5b4fdddcd0d4f0eda4a74ebe">BinaryHeap</a>
, <a class="el" href="class_binary_heap___four_ints.html#a5205fb4581fad5ba22013cc77af56670">BinaryHeap_FourInts</a>
, <a class="el" href="class_binary_heap___int_key___two_ints.html#afc1db8650e6d9410f3924d48061c4c5e">BinaryHeap_IntKey_TwoInts</a>
, <a class="el" href="class_binary_heap___two_ints.html#a81fe1d180e77658e1473317fc7a85fa3">BinaryHeap_TwoInts</a>
</li>
</ul>


<h3><a id="index_n"></a>- n -</h3><ul>
<li>Node()
: <a class="el" href="class_node.html#a439595ca0e98fe92ee87a54b509a7810">Node</a>
</li>
</ul>


<h3><a id="index_p"></a>- p -</h3><ul>
<li>pop()
: <a class="el" href="class_stack.html#ad2d05ce55e7abd4a8d8ea1263be99675">Stack</a>
</li>
<li>prepare()
: <a class="el" href="class_array_heap_ext_mem.html#a28f40b2225137d0f8cbd0c065f767e4b">ArrayHeapExtMem</a>
</li>
<li>push()
: <a class="el" href="class_stack.html#afbe7194689ec0e63b2ab3243db2ff08f">Stack</a>
</li>
</ul>


<h3><a id="index_r"></a>- r -</h3><ul>
<li>read()
: <a class="el" href="class_distance_reader.html#afecfe4aef179860eacda30ed521e7573">DistanceReader</a>
, <a class="el" href="class_distance_reader_ext_mem.html#aa0722c8fe7fc51b8f074ca7d294ffd74">DistanceReaderExtMem</a>
</li>
<li>readAndWrite()
: <a class="el" href="class_distance_reader.html#a556884960e4de69a39078d2ef642f5a1">DistanceReader</a>
</li>
<li>removeMin()
: <a class="el" href="class_array_heap_ext_mem.html#a7a233b3fbadb58b060a9147097a2c38e">ArrayHeapExtMem</a>
, <a class="el" href="class_candidate_heap.html#a149d883abbb968518621afe4e8a62753">CandidateHeap</a>
</li>
</ul>


<h3><a id="index_s"></a>- s -</h3><ul>
<li>SequenceFileReader()
: <a class="el" href="class_sequence_file_reader.html#afefc977e0ab5e10c56afbf0f2fa2ada8">SequenceFileReader</a>
</li>
<li>size()
: <a class="el" href="class_array_heap_ext_mem.html#a26fc220d8364d7e8894c3f5717714a51">ArrayHeapExtMem</a>
, <a class="el" href="class_binary_heap.html#a903e4bbeaa9ca7cb7baa5a22730cd45a">BinaryHeap</a>
, <a class="el" href="class_binary_heap___four_ints.html#a18289cc0bc8da385f74d2301aff90dc1">BinaryHeap_FourInts</a>
, <a class="el" href="class_binary_heap___int_key___two_ints.html#a331deccbe55e80bfb1b966be6843406c">BinaryHeap_IntKey_TwoInts</a>
, <a class="el" href="class_binary_heap___two_ints.html#a7591ee0a24dd8dd6bb904b4ead51ff04">BinaryHeap_TwoInts</a>
</li>
<li>SlotPair()
: <a class="el" href="class_slot_pair.html#ac09540de71ab2af1b8ec8265f1453760">SlotPair</a>
</li>
<li>Stack()
: <a class="el" href="class_stack.html#a14cd1cba325bead4ff0a91bc6eb0f6f5">Stack</a>
</li>
</ul>


<h3><a id="index_t"></a>- t -</h3><ul>
<li>test()
: <a class="el" href="class_array_heap_ext_mem.html#abedb647d18a126923c1de65ed5a550ca">ArrayHeapExtMem</a>
</li>
<li>testDifferenceCluster()
: <a class="el" href="class_distance_calculator.html#ac315efce21a47f3e77fb61ea933f930b">DistanceCalculator</a>
</li>
<li>TreeBuilder()
: <a class="el" href="class_tree_builder.html#a50223a97cf2e33142ced2c212e22cad6">TreeBuilder</a>
</li>
<li>TreeBuilderBinHeap()
: <a class="el" href="class_tree_builder_bin_heap.html#abbd80cd829cf7f5187fb6bfa7057256c">TreeBuilderBinHeap</a>
</li>
<li>TreeBuilderExtMem()
: <a class="el" href="class_tree_builder_ext_mem.html#a097a3625841011bcb55bc8663696b6de">TreeBuilderExtMem</a>
</li>
<li>TreeBuilderManager()
: <a class="el" href="class_tree_builder_manager.html#a1c1e9bc07025dd5160ac37277c10647a">TreeBuilderManager</a>
</li>
<li>TreeNode()
: <a class="el" href="class_tree_node.html#a984a98d5ccf7ef1f5a18094c6821f35d">TreeNode</a>
</li>
</ul>


<h3><a id="index_w"></a>- w -</h3><ul>
<li>write()
: <a class="el" href="class_distance_reader.html#ac6c565a94488665715dac977d32353a2">DistanceReader</a>
</li>
</ul>


<h3><a id="index__7E"></a>- ~ -</h3><ul>
<li>~ArrayHeapExtMem()
: <a class="el" href="class_array_heap_ext_mem.html#a24ce2bacde78413e6db5bb7b2e45a95e">ArrayHeapExtMem</a>
</li>
<li>~BinaryHeap()
: <a class="el" href="class_binary_heap.html#a0bfd6a2f831b7d4282be2ec3838f0af5">BinaryHeap</a>
</li>
<li>~BinaryHeap_FourInts()
: <a class="el" href="class_binary_heap___four_ints.html#ad314090461a237a95b7e9060eb8547c6">BinaryHeap_FourInts</a>
</li>
<li>~BinaryHeap_IntKey_TwoInts()
: <a class="el" href="class_binary_heap___int_key___two_ints.html#aec27628d47ff3b470ccd44c1e337365a">BinaryHeap_IntKey_TwoInts</a>
</li>
<li>~BinaryHeap_TwoInts()
: <a class="el" href="class_binary_heap___two_ints.html#a1fa71262df0bb9bf2c9b6266eb9af356">BinaryHeap_TwoInts</a>
</li>
<li>~CandidateHeap()
: <a class="el" href="class_candidate_heap.html#abdbcc88328c293641d76c8a26f5e54e9">CandidateHeap</a>
</li>
<li>~DistanceCalculator()
: <a class="el" href="class_distance_calculator.html#a937924271f1403a83408b4807589bd91">DistanceCalculator</a>
</li>
<li>~DistanceReader()
: <a class="el" href="class_distance_reader.html#afb8cba60a6bcf7f4814d297be76b9cb5">DistanceReader</a>
</li>
<li>~SequenceFileReader()
: <a class="el" href="class_sequence_file_reader.html#a68f93cafb0fff8017a6ddfdac763b2ec">SequenceFileReader</a>
</li>
<li>~Stack()
: <a class="el" href="class_stack.html#a40bd5dff912f0e5290777c4b46d17809">Stack</a>
</li>
<li>~TreeBuilder()
: <a class="el" href="class_tree_builder.html#aaf3859d93a39df4713024db0efd6dc0a">TreeBuilder</a>
</li>
<li>~TreeBuilderBinHeap()
: <a class="el" href="class_tree_builder_bin_heap.html#af7ddcc75b903a4a5cd43541543a7ad60">TreeBuilderBinHeap</a>
</li>
<li>~TreeBuilderExtMem()
: <a class="el" href="class_tree_builder_ext_mem.html#a1a01122703a9e481d4d2b441a32accd0">TreeBuilderExtMem</a>
</li>
<li>~TreeNode()
: <a class="el" href="class_tree_node.html#a138449d182c342d032c78e7037afc151">TreeNode</a>
</li>
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